Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g02363.F4
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3166
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Found at i:1288 original size:98 final size:98
Alignment explanation
Indices: 1119--1313 Score: 266
Period size: 98 Copynumber: 2.0 Consensus size: 98
1109 ACCCTAACGG
* * ** *
1119 TTTGTTCGATTAGCTGAAATTTGGTTGCTCGGTTAATTCGAGAATATTGCTATATTCATTGTTTG
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGGTTG
* *
1184 TTTAAGATTATCATAGAATGTGTAGGAGCATGT
66 TTTAAGATGATCATACAATGTGTAGGAGCATGT
* * *
1217 TTTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGT-ATTGGTT
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATAT-TCATTGGTT
* *
1281 GTTTAAGATGATGATACATTGTGTAGGAGCATG
65 GTTTAAGATGATCATACAATGTGTAGGAGCATG
1314 CTTTCTTCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 83 0.99
99 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (98 bp):
TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGGTTG
TTTAAGATGATCATACAATGTGTAGGAGCATGT
Found at i:1532 original size:186 final size:185
Alignment explanation
Indices: 1218--1858 Score: 933
Period size: 186 Copynumber: 3.4 Consensus size: 185
1208 GGAGCATGTT
* * * * * * *
1218 TTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGTATTGGTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
1283 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
1348 GAACTGTTTATATGCTGCTTCTGAGTCTGCTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTG-TGAGGCTGCTAATCAACCCCAAAGGC
* ** ** *
1404 TTGTTCGGTTAGCTGAAATTCAATTGCTCGGTTAATTTGAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
*
1469 TTAAGACGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* *
1534 GAGCTGTTTATATGCTGCTTCCGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTG-TGAGGCTGCTAATCAACCCCAAAGGC
* *
1590 TTGTTCCATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* * * *
1655 CTAAGATGATGATACATAGTGTAGGAGCATACTTTCTTCAGTATGAATCTCATTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* * * *
1720 GAACT-TTCTATATGCTGCTGCTGAGTCTGTGGAGGCTACTAATCAACCCTAAAGGT
131 GAACTGTT-TATATGCTGCTTCTGAGTCTGT-GAGGCTGCTAATCAACCCCAAAGGC
* ** * **
1776 TTGTTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* *
1841 TTTAGATGATAATACATT
66 TTAAGATGATGATACATT
1859 TTTTAGTAGT
Statistics
Matches: 410, Mismatches: 43, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
185 3 0.01
186 407 0.99
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (185 bp):
TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
GAACTGTTTATATGCTGCTTCTGAGTCTGTGAGGCTGCTAATCAACCCCAAAGGC
Found at i:1954 original size:98 final size:98
Alignment explanation
Indices: 1779--1956 Score: 227
Period size: 98 Copynumber: 1.8 Consensus size: 98
1769 TAAAGGTTTG
* * *
1779 TTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGTTTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
1844 AGATGATAATACATTTTTTAGTAGTATGTTTTC
66 AGATGATAATACATTTTTTAGTAGTATGTTTTC
* ** * *
1877 TTCATTTAGCTGAAATTAGATTGCTCGGTTAATTCGAGAATTC-TGGC-ATATTTATTGTTTGTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAA--CATGGCTATATGTATTGTTTGTT
*
1940 TAA-AGTGATGATACATT
64 TAAGA-TGATAATACATT
1957 GTGTAGGAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 1 0.01
98 63 0.93
99 3 0.04
100 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (98 bp):
TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
AGATGATAATACATTTTTTAGTAGTATGTTTTC
Found at i:1975 original size:98 final size:98
Alignment explanation
Indices: 1779--1978 Score: 217
Period size: 98 Copynumber: 2.0 Consensus size: 98
1769 TAAAGGTTTG
* * *
1779 TTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGTTTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
* * * * * *
1844 AGATGATAATACATTTTTTAGTAGTATGTTTTC
66 AGATGATAATACATTGTGTAGGAGCACGCTTTC
* ** * *
1877 TTCATTTAGCTGAAATTAGATTGCTCGGTTAATTCGAGAATTC-TGGC-ATATTTATTGTTTGTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAA--CATGGCTATATGTATTGTTTGTT
*
1940 TAA-AGTGATGATACATTGTGTAGGAGCACGCTTTC
64 TAAGA-TGATAATACATTGTGTAGGAGCACGCTTTC
1975 TTCA
1 TTCA
1979 GAATGAATCT
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
97 1 0.01
98 79 0.94
99 3 0.04
100 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (98 bp):
TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
AGATGATAATACATTGTGTAGGAGCACGCTTTC
Found at i:2390 original size:23 final size:23
Alignment explanation
Indices: 2360--2408 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2350 CTCCCCAATG
2360 CTACTTTCTCTGCCCACAAGACT
1 CTACTTTCTCTGCCCACAAGACT
2383 CTACTTTCTCTGCCCACAAGACT
1 CTACTTTCTCTGCCCACAAGACT
2406 CTA
1 CTA
2409 ACCCAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.08, T:0.31
Consensus pattern (23 bp):
CTACTTTCTCTGCCCACAAGACT
Done.